RetrogeneDB ID: retro_hsap_62

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 12:117013747..117014125(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000171471
• Aliases: MAP1LC3B2, ATG8G
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MAP1LC3B
• Ensembl ID: ENSG00000140941
• Aliases: MAP1LC3B, ATG8F, LC3B, MAP1A/1BLC3, MAP1LC3B-a
• Description: microtubule-associated protein 1 light chain 3 beta [Source:HGNC Symbol;Acc:13352]

Sequence

>retro_hsap_62
ATGCCGTCGGAGAAGACCTTCAAGCAGCGGCGCACCTTCGAACAAAGAGTAGAAGATGTCCGACTTATTCGAGAGCAGCA
TCCAACCAAAATCCCGGTGATAATAGAACGATACAAGGGTGAGAAGCAGCTTCCTGTTCTGGATAAAACAAAGTTCCTTG
TACCTGACCATGTCAACATGAGTGAGCTCATCAAGATAATTAGAAGGCGCTTACAGCTCAATGCTAATCAGGCCTTCTTC
CTGTTGGTGAACGGACACAGCATGGTCAGCGTCTCCACACCAATCTCAGAGGTGTATGAGAGTGAGAAAGATGAAGATGG
ATTCCTGTACATGGTCTGTGCCTCCCAGGAGACGTTCGGGATGAAATTGTCAGTGTAA

Alignment

ORF - retro_hsap_62 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.2 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRR
          MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRR
Retrocopy MPSEKTFKQRRTFEQRVEDVRLIREQHPTKIPVIIERYKGEKQLPVLDKTKFLVPDHVNMSELIKIIRRR

Parental  LQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVYASQETFGMKLSV
          LQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMV.ASQETFGMKLSV
Retrocopy LQLNANQAFFLLVNGHSMVSVSTPISEVYESEKDEDGFLYMVCASQETFGMKLSV

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
bodymap2_adipose	2.82 RPM	251.65 RPM
bodymap2_adrenal	0.80 RPM	76.51 RPM
bodymap2_brain	2.34 RPM	224.35 RPM
bodymap2_breast	0.68 RPM	97.51 RPM
bodymap2_colon	1.64 RPM	125.66 RPM
bodymap2_heart	0.37 RPM	155.39 RPM
bodymap2_kidney	0.85 RPM	100.75 RPM
bodymap2_liver	0.53 RPM	39.01 RPM
bodymap2_lung	1.11 RPM	174.05 RPM
bodymap2_lymph_node	0.35 RPM	128.77 RPM
bodymap2_ovary	0.81 RPM	58.93 RPM
bodymap2_prostate	0.81 RPM	130.00 RPM
bodymap2_skeletal_muscle	1.38 RPM	175.19 RPM
bodymap2_testis	1.96 RPM	111.37 RPM
bodymap2_thyroid	2.01 RPM	142.65 RPM
bodymap2_white_blood_cells	1.48 RPM	164.08 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_62 was not detected

EST

No EST(s) were mapped for retro_hsap_62 retrocopy.

TSS

No TSS is located nearby retro_hsap_62 retrocopy 5' end.

Lab

retro_hsap_62 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_62 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_63

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Parental genes homology:

Parental genes homology involve 32 parental genes, and 96 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018254	2 retrocopies	retro_amel_1660, retro_amel_873,
Bos taurus	ENSBTAG00000011632	1 retrocopy	retro_btau_977,
Canis familiaris	ENSCAFG00000019909	1 retrocopy	retro_cfam_1578,
Choloepus hoffmanni	ENSCHOG00000012090	7 retrocopies	retro_chof_146, retro_chof_2230, retro_chof_2274, retro_chof_2432, retro_chof_510, retro_chof_558, retro_chof_960,
Callithrix jacchus	ENSCJAG00000004473	3 retrocopies	retro_cjac_1114, retro_cjac_1519, retro_cjac_779,
Cavia porcellus	ENSCPOG00000023922	1 retrocopy	retro_cpor_394,
Dasypus novemcinctus	ENSDNOG00000010228	7 retrocopies	retro_dnov_1008, retro_dnov_1024, retro_dnov_1335, retro_dnov_165, retro_dnov_2435, retro_dnov_2604, retro_dnov_913,
Dipodomys ordii	ENSDORG00000013862	1 retrocopy	retro_dord_376,
Echinops telfairi	ENSETEG00000015189	2 retrocopies	retro_etel_1050, retro_etel_3,
Felis catus	ENSFCAG00000001938	4 retrocopies	retro_fcat_1727, retro_fcat_1874, retro_fcat_340, retro_fcat_884,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Homo sapiens	ENSG00000139112	1 retrocopy	retro_hsap_60,
Homo sapiens	ENSG00000140941	3 retrocopies	retro_hsap_3695, retro_hsap_487, retro_hsap_62 ,
Loxodonta africana	ENSLAFG00000023364	3 retrocopies	retro_lafr_1077, retro_lafr_915, retro_lafr_974,
Microcebus murinus	ENSMICG00000007356	2 retrocopies	retro_mmur_117, retro_mmur_507,
Myotis lucifugus	ENSMLUG00000015596	1 retrocopy	retro_mluc_1586,
Macaca mulatta	ENSMMUG00000017613	1 retrocopy	retro_mmul_15,
Mus musculus	ENSMUSG00000031812	4 retrocopies	retro_mmus_1271, retro_mmus_2384, retro_mmus_2619, retro_mmus_846,
Nomascus leucogenys	ENSNLEG00000011511	4 retrocopies	retro_nleu_1032, retro_nleu_1467, retro_nleu_2392, retro_nleu_931,
Oryctolagus cuniculus	ENSOCUG00000022970	4 retrocopies	retro_ocun_1155, retro_ocun_572, retro_ocun_731, retro_ocun_784,
Otolemur garnettii	ENSOGAG00000004256	3 retrocopies	retro_ogar_1468, retro_ogar_2885, retro_ogar_2892,
Ochotona princeps	ENSOPRG00000015461	4 retrocopies	retro_opri_1136, retro_opri_369, retro_opri_85, retro_opri_977,
Pongo abelii	ENSPPYG00000007628	7 retrocopies	retro_pabe_1280, retro_pabe_1566, retro_pabe_245, retro_pabe_3157, retro_pabe_3158, retro_pabe_940, retro_pabe_978,
Pan troglodytes	ENSPTRG00000008445	3 retrocopies	retro_ptro_2505, retro_ptro_367, retro_ptro_63,
Pteropus vampyrus	ENSPVAG00000016858	1 retrocopy	retro_pvam_728,
Rattus norvegicus	ENSRNOG00000017905	5 retrocopies	retro_rnor_1240, retro_rnor_1739, retro_rnor_1865, retro_rnor_1868, retro_rnor_2033,
Sarcophilus harrisii	ENSSHAG00000017074	1 retrocopy	retro_shar_168,
Sus scrofa	ENSSSCG00000002655	2 retrocopies	retro_sscr_188, retro_sscr_737,
Ictidomys tridecemlineatus	ENSSTOG00000014826	2 retrocopies	retro_itri_1505, retro_itri_662,
Tupaia belangeri	ENSTBEG00000001165	11 retrocopies	retro_tbel_1008, retro_tbel_1644, retro_tbel_2020, retro_tbel_2484, retro_tbel_2561, retro_tbel_3181, retro_tbel_3301, retro_tbel_636, retro_tbel_706, retro_tbel_733, retro_tbel_990,
Tursiops truncatus	ENSTTRG00000008821	2 retrocopies	retro_ttru_1336, retro_ttru_1454,
Vicugna pacos	ENSVPAG00000010065	2 retrocopies	retro_vpac_169, retro_vpac_186,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.30 RPM
CEU_NA11843	0.14 RPM
CEU_NA11930	0.55 RPM
CEU_NA12004	0.38 RPM
CEU_NA12400	0.49 RPM
CEU_NA12751	0.32 RPM
CEU_NA12760	0.31 RPM
CEU_NA12827	0.14 RPM
CEU_NA12872	0.35 RPM
CEU_NA12873	0.22 RPM
FIN_HG00183	0.33 RPM
FIN_HG00277	0.07 RPM
FIN_HG00315	0.17 RPM
FIN_HG00321	0.18 RPM
FIN_HG00328	0.28 RPM
FIN_HG00338	0.19 RPM
FIN_HG00349	0.20 RPM
FIN_HG00375	0.10 RPM
FIN_HG00377	0.25 RPM
FIN_HG00378	0.34 RPM
GBR_HG00099	0.12 RPM
GBR_HG00111	0.13 RPM
GBR_HG00114	0.13 RPM
GBR_HG00119	0.26 RPM
GBR_HG00131	0.57 RPM
GBR_HG00133	0.12 RPM
GBR_HG00134	0.13 RPM
GBR_HG00137	0.08 RPM
GBR_HG00142	0.14 RPM
GBR_HG00143	0.16 RPM
TSI_NA20512	0.17 RPM
TSI_NA20513	0.17 RPM
TSI_NA20518	0.33 RPM
TSI_NA20532	0.27 RPM
TSI_NA20538	0.23 RPM
TSI_NA20756	0.41 RPM
TSI_NA20765	0.29 RPM
TSI_NA20771	0.34 RPM
TSI_NA20786	0.47 RPM
TSI_NA20798	0.19 RPM
YRI_NA18870	0.41 RPM
YRI_NA18907	0.00 RPM
YRI_NA18916	0.25 RPM
YRI_NA19093	0.26 RPM
YRI_NA19099	0.21 RPM
YRI_NA19114	0.52 RPM
YRI_NA19118	0.21 RPM
YRI_NA19213	0.43 RPM
YRI_NA19214	0.05 RPM
YRI_NA19223	0.14 RPM

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Indel association:

No indels were associated with its genomic coordinates. Based on Kabza et al. 2015 (PubMed).