RetrogeneDB ID: retro_ptro_2828

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 9:39146139..39146871(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: YWHAB
• Ensembl ID: ENSPTRG00000013529
• Aliases: None
• Description: tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, beta polypeptide [Source:HGNC Symbol;Acc:12849]

Sequence

>retro_ptro_2828
GTGACAATGGATAAAAGTGTGCTGGTACAGAAAGCCAGGCCCGCTGAGCAGGCTGAGCGCGGTGATGATGTGGCTGCAGC
CGGGAAGGCAGCCATGCCACAGGGGCATGCGCCCCCAGCTGAAGACAGCAATCTGCCCTCTGCCGCCTACAAGAATATGG
TGGGGCCCACTGTTCTTCCTGGATTCTCATCTCCAGCACTGAGCAGAGAACAGGAGGAATGAGAAGCAGCAGATGGGCAA
AGAGTACCATGGAAGACAGAGGCAGAGCTGCTGGACATCTGCAATGAAGTTCCGGAGCTGTTGGACAAGTCTCTTATTCC
CCATGCTACGCAACCTGAAAGCAAGGCGTTCTCCTTGAAAATGAAAGGAGATTGTTTCAGGTATCTTTCTGGGGTGGCGT
CTGGAGACAATAAACAAACCACACTGTTGAACTCCCAGCAGGCTTACCAGGAAACATCTGAAATTAGTAAGAAAGATATG
CAGCCTACACACCCAATTCGACTGGGCCTGGCACTTAATTTCTCAGTCTTTTGCTACGGGATTCTAAACTCTCCTGAAAA
GGCCTGCAGCCTGGCAAACATGGCATTTGATGAAGCAATTGCTGAGTTGGATACACTGAATGAAGAGTCTTATAAAGACA
GCACTCCCACCATGCAGTGACTTCGGGACAATCTCACTCTGTGGACATTGGGAAACCAGGGAGATGCAGGAGATGCTGGG
GAGGGAGAGAAC

Alignment

ORF - retro_ptro_2828 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.11 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MTMDKSELVQKAKLAEQAERYDDMAAAMKAVTEQGHELSNEERNLLSVAYKNVVG-ARRSSWRVISSIEQ
          .TMDKS.LVQKA..AEQAER.DD.AAA.KA...QGH....E..NL.S.AYKN.VG.A..SSW..ISS.EQ
Retrocopy VTMDKSVLVQKARPAEQAERGDDVAAAGKAAMPQGHAPPAEDSNLPSAAYKNMVG<AHCSSWILISSTEQ

Parental  KT-ERNEKKQQMGKEYRE-KIEAELQDICNDVLELLDKYLIPNATQPESKVFYLKMKGDYFRYLSEVASG
          .T..RNEK.QQMGKEY...K.EAEL.DICN.V.ELLDK.LIP.ATQPESK.F.LKMKGD.FRYLS.VASG
Retrocopy RT<RRNEK-QQMGKEYHG<KTEAELLDICNEVPELLDKSLIPHATQPESKAFSLKMKGDCFRYLSGVASG

Parental  DNKQTTVSNSQQAYQEAFEISKKEMQPTHPIRLGLALNFSVFYYEILNSPEKACSLAKTAFDEAIAELDT
          DNKQTT..NSQQAYQE..EISKK.MQPTHPIRLGLALNFSVF.Y.ILNSPEKACSLA..AFDEAIAELDT
Retrocopy DNKQTTLLNSQQAYQETSEISKKDMQPTHPIRLGLALNFSVFCYGILNSPEKACSLANMAFDEAIAELDT

Parental  LNEESYKDSTLIMQLLRDNLTLWTSENQGDEGDAGEGEN
          LNEESYKDST..MQ.LRDNLTLWT..NQGD.GDAGEGEN
Retrocopy LNEESYKDSTPTMQ*LRDNLTLWTLGNQGDAGDAGEGEN

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
SRP007412_brain_prefrontal_cortex	0.73 RPM	344.89 RPM
SRP007412_cerebellum	1.86 RPM	282.74 RPM
SRP007412_heart	0.00 RPM	140.57 RPM
SRP007412_kidney	0.08 RPM	222.42 RPM
SRP007412_liver	0.03 RPM	119.81 RPM
SRP007412_testis	0.00 RPM	83.89 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2828 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2828 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2828 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 27 parental genes, and 146 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011796	1 retrocopy	retro_acar_8,
Choloepus hoffmanni	ENSCHOG00000005782	15 retrocopies	retro_chof_1049, retro_chof_1325, retro_chof_1630, retro_chof_1670, retro_chof_1975, retro_chof_22, retro_chof_2221, retro_chof_2350, retro_chof_2423, retro_chof_2619, retro_chof_326, retro_chof_352, retro_chof_487, retro_chof_707, retro_chof_971,
Callithrix jacchus	ENSCJAG00000017664	2 retrocopies	retro_cjac_1002, retro_cjac_2214,
Dipodomys ordii	ENSDORG00000001064	14 retrocopies	retro_dord_235, retro_dord_236, retro_dord_255, retro_dord_256, retro_dord_258, retro_dord_259, retro_dord_262, retro_dord_263, retro_dord_332, retro_dord_442, retro_dord_545, retro_dord_681, retro_dord_725, retro_dord_9,
Echinops telfairi	ENSETEG00000009967	4 retrocopies	retro_etel_1221, retro_etel_1380, retro_etel_1536, retro_etel_1705,
Homo sapiens	ENSG00000166913	4 retrocopies	retro_hsap_4160, retro_hsap_4841, retro_hsap_622, retro_hsap_855,
Gorilla gorilla	ENSGGOG00000004580	2 retrocopies	retro_ggor_2795, retro_ggor_699,
Microcebus murinus	ENSMICG00000000973	7 retrocopies	retro_mmur_1044, retro_mmur_1100, retro_mmur_1288, retro_mmur_1576, retro_mmur_27, retro_mmur_305, retro_mmur_979,
Myotis lucifugus	ENSMLUG00000006319	1 retrocopy	retro_mluc_871,
Macaca mulatta	ENSMMUG00000013206	3 retrocopies	retro_mmul_1061, retro_mmul_236, retro_mmul_673,
Monodelphis domestica	ENSMODG00000016200	2 retrocopies	retro_mdom_1557, retro_mdom_212,
Nomascus leucogenys	ENSNLEG00000006643	2 retrocopies	retro_nleu_42, retro_nleu_422,
Oryctolagus cuniculus	ENSOCUG00000003002	1 retrocopy	retro_ocun_273,
Otolemur garnettii	ENSOGAG00000008909	3 retrocopies	retro_ogar_122, retro_ogar_1243, retro_ogar_2934,
Ochotona princeps	ENSOPRG00000011836	2 retrocopies	retro_opri_56, retro_opri_924,
Pongo abelii	ENSPPYG00000011041	5 retrocopies	retro_pabe_3453, retro_pabe_3454, retro_pabe_3519, retro_pabe_3520, retro_pabe_692,
Pan troglodytes	ENSPTRG00000008521	5 retrocopies	retro_ptro_1697, retro_ptro_2538, retro_ptro_2624, retro_ptro_2626, retro_ptro_2993,
Pan troglodytes	ENSPTRG00000011641	2 retrocopies	retro_ptro_2032, retro_ptro_3,
Pan troglodytes	ENSPTRG00000013529	12 retrocopies	retro_ptro_1010, retro_ptro_1686, retro_ptro_2390, retro_ptro_2828 , retro_ptro_2887, retro_ptro_3125, retro_ptro_3201, retro_ptro_3225, retro_ptro_412, retro_ptro_453, retro_ptro_594, retro_ptro_965,
Pteropus vampyrus	ENSPVAG00000012662	1 retrocopy	retro_pvam_157,
Sarcophilus harrisii	ENSSHAG00000011241	1 retrocopy	retro_shar_483,
Sus scrofa	ENSSSCG00000007381	1 retrocopy	retro_sscr_506,
Ictidomys tridecemlineatus	ENSSTOG00000003733	1 retrocopy	retro_itri_1214,
Tupaia belangeri	ENSTBEG00000002806	47 retrocopies	retro_tbel_1038, retro_tbel_1272, retro_tbel_1460, retro_tbel_1472, retro_tbel_1572, retro_tbel_1653, retro_tbel_1664, retro_tbel_2127, retro_tbel_2128, retro_tbel_2229, retro_tbel_2246, retro_tbel_228, retro_tbel_2371, retro_tbel_2373, retro_tbel_2379, retro_tbel_2397, retro_tbel_2512, retro_tbel_2536, retro_tbel_2540, retro_tbel_2542, retro_tbel_2583, retro_tbel_2584, retro_tbel_2615, retro_tbel_2617, retro_tbel_3502, retro_tbel_3554, retro_tbel_3604, retro_tbel_3642, retro_tbel_3743, retro_tbel_390, retro_tbel_3989, retro_tbel_3993, retro_tbel_40, retro_tbel_4101, retro_tbel_4121, retro_tbel_4338, retro_tbel_4447, retro_tbel_4456, retro_tbel_4459, retro_tbel_4510, retro_tbel_4514, retro_tbel_4604, retro_tbel_4664, retro_tbel_4690, retro_tbel_5, retro_tbel_705, retro_tbel_854,
Tarsius syrichta	ENSTSYG00000006537	4 retrocopies	retro_tsyr_1065, retro_tsyr_1473, retro_tsyr_1637, retro_tsyr_2084,
Tursiops truncatus	ENSTTRG00000007615	1 retrocopy	retro_ttru_762,
Vicugna pacos	ENSVPAG00000005023	3 retrocopies	retro_vpac_396, retro_vpac_516, retro_vpac_9,