RetrogeneDB ID: retro_hsap_777

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 11:43919317..43920419(+)
• Located in intron of: ENSG00000166199

Retrocopy information

• Ensembl ID: ENSG00000213693
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SEC14L1
• Ensembl ID: ENSG00000129657
• Aliases: SEC14L1, PRELID4A, SEC14L
• Description: SEC14-like 1 (S. cerevisiae) [Source:HGNC Symbol;Acc:10698]

Sequence

>retro_hsap_777
TGCTATACCGTTCACCCTGAAAATGAAGATTGGACCCGTTTTGAACAGTCTGCAAGTTTAGATATTAAATCTTTCTTTGG
TTTTGAAAGTACCATGGAAAAAATTGCAATGAAACAATATACCAGCAATATTAAAAAAAGGAAAGAAAATTATTGAATAC
TACCTTCGCCATTTAGAAGGAGGCATAACCTTTGTGCCCCATTGGACTCCACCTTCCATCACGCCCTCTTCAGAGACATC
TTCGTCATCCTGCAAGAAACAAGCAGCGTCCATGGCTGTTGTCATCCCAGATGCTGTCCTCAAGGAGGGGCTGAGTGGCG
ATGCCCTCAGCAGCCCCAGTGCACCTGAGCCCGTGGTGGGCATCCCTGATAACAAACTAGATGCTGACTACATCAAGAGA
TACCTGGGCGATTTGACTCCGCTGCAGGAGAGCTGTCTCATTAGACTTCACGGGTGGCTCCAGGAGACCCACAAGGGTGA
AATTCCAAAAGATGAGCATATTCTTCAGTTCCTATGTGCATGGGATTTTAATATTGACAAAGCCAGAGAGATCATTTGTC
AATCTTTGGCGTGGAGGAAGCAGCACCAGGTAGACTACATTCTTGCTACCTGGGCCGTTCCACAGGTCCTTCAGAATTAC
TACACGGGAGGCTGGCATCATCACGACAAAGATGGGTGGCCCCTCTGTATGCTCAGGCTGGGGCAGATGGACACCAACGG
CTTGGTGAGAGCACTCGGGGAGGAAGCCCTGCTGAGATACGTTCTCTCCATAAATGAAGAAGAGCTAAGGCGATGTGAAG
AGAATACAAAAGTCTTTGTTTGGCCTATCAGCTCATGGACCTGCCTGGCGGACTTGGAAGGGGTGAACATGCGCCACTTA
TGGAGACCTGATGTCAAAGTGCTGCGGTGGATCATCGAGGTGGTGAAGGCCAGTTACCCTAAGAGACTGGGCCGACTTCT
CATCCTGCGGTCACCCAGGGTATTTCCTGTGCTCTGGACGCTGGTTAGTCCATTTATTGATGACAACACCAGAAGGAAAT
TCCTCATTTATGCAGGAAATGACTACCAGGGTCCTGGAGGCCTGCTGGATTACATTGATAGA

Alignment

ORF - retro_hsap_777 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.26 %
• Parental protein coverage: 51.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  CYTVHPENEDWTCFEQSASLDIKSFFGFESTVEKIAMKQYTSNIKK-GKEIIEYYLRQLEEEGITFVPRW
          CYTVHPENEDWT.FEQSASLDIKSFFGFEST.EKIAMKQYTSNIKK.GK.IIEYYLR.LE..GITFVP.W
Retrocopy CYTVHPENEDWTRFEQSASLDIKSFFGFESTMEKIAMKQYTSNIKK>GKKIIEYYLRHLEG-GITFVPHW

Parental  SPPSITTSSETSSSSSKKQAASMAVVIPEAALKEGLSGDALSSPSAPEPVVGTPDDKLDADYIKRYLGDL
          .PPSIT.SSETSSSS.KKQAASMAVVIP.A.LKEGLSGDALSSPSAPEPVVG.PD.KLDADYIKRYLGDL
Retrocopy TPPSITPSSETSSSSCKKQAASMAVVIPDAVLKEGLSGDALSSPSAPEPVVGIPDNKLDADYIKRYLGDL

Parental  TPLQESCLIRLRQWLQETHKGKIPKDEHILRFLRARDFNIDKAREIMCQSLTWRKQHQVDYILETWTPPQ
          TPLQESCLIRL..WLQETHKG.IPKDEHIL.FL.A.DFNIDKAREI.CQSL.WRKQHQVDYIL.TW..PQ
Retrocopy TPLQESCLIRLHGWLQETHKGEIPKDEHILQFLCAWDFNIDKAREIICQSLAWRKQHQVDYILATWAVPQ

Parental  VLQDYYAGGWHHHDKDGRPLYVLRLGQMDTKGLVRALGEEALLRYVLSINEEGLRRCEENTKVFGRPISS
          VLQ.YY.GGWHHHDKDG.PL..LRLGQMDT.GLVRALGEEALLRYVLSINEE.LRRCEENTKVF..PISS
Retrocopy VLQNYYTGGWHHHDKDGWPLCMLRLGQMDTNGLVRALGEEALLRYVLSINEEELRRCEENTKVFVWPISS

Parental  WTCLVDLEGLNMRHLWRPGVKALLRIIEVVEANYPETLGRLLILRAPRVFPVLWTLVSPFIDDNTRRKFL
          WTCL.DLEG.NMRHLWRP.VK.L..IIEVV.A.YP..LGRLLILR.PRVFPVLWTLVSPFIDDNTRRKFL
Retrocopy WTCLADLEGVNMRHLWRPDVKVLRWIIEVVKASYPKRLGRLLILRSPRVFPVLWTLVSPFIDDNTRRKFL

Parental  IYAGNDYQGPGGLLDYIDK
          IYAGNDYQGPGGLLDYID.
Retrocopy IYAGNDYQGPGGLLDYIDR

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	0.14 RPM	398.31 RPM
bodymap2_adrenal	0.84 RPM	117.94 RPM
bodymap2_brain	0.47 RPM	138.51 RPM
bodymap2_breast	0.51 RPM	102.22 RPM
bodymap2_colon	0.15 RPM	181.12 RPM
bodymap2_heart	0.06 RPM	91.51 RPM
bodymap2_kidney	0.15 RPM	245.39 RPM
bodymap2_liver	0.00 RPM	43.77 RPM
bodymap2_lung	0.02 RPM	397.35 RPM
bodymap2_lymph_node	0.02 RPM	208.67 RPM
bodymap2_ovary	1.02 RPM	74.00 RPM
bodymap2_prostate	0.48 RPM	75.38 RPM
bodymap2_skeletal_muscle	0.00 RPM	81.14 RPM
bodymap2_testis	0.51 RPM	150.84 RPM
bodymap2_thyroid	0.32 RPM	119.73 RPM
bodymap2_white_blood_cells	0.08 RPM	327.37 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_hsap_777 was not detected

EST

1 EST(s) were mapped to retro_hsap_777 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG112955	43919537	43919990	100	453	0	453

TSS

No TSS is located nearby retro_hsap_777 retrocopy 5' end.

Lab

retro_hsap_777 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_777 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000129657	1 retrocopy	retro_hsap_777 ,
Nomascus leucogenys	ENSNLEG00000007634	1 retrocopy	retro_nleu_403,
Pongo abelii	ENSPPYG00000008673	1 retrocopy	retro_pabe_752,

Population studies

Expression level across human populations :

Library	Retrogene expression
CEU_NA11831	0.64 RPM
CEU_NA11843	0.43 RPM
CEU_NA11930	0.72 RPM
CEU_NA12004	0.08 RPM
CEU_NA12400	0.56 RPM
CEU_NA12751	0.73 RPM
CEU_NA12760	0.40 RPM
CEU_NA12827	0.52 RPM
CEU_NA12872	0.54 RPM
CEU_NA12873	0.32 RPM
FIN_HG00183	0.71 RPM
FIN_HG00277	0.70 RPM
FIN_HG00315	0.55 RPM
FIN_HG00321	0.60 RPM
FIN_HG00328	0.38 RPM
FIN_HG00338	0.45 RPM
FIN_HG00349	0.43 RPM
FIN_HG00375	0.44 RPM
FIN_HG00377	0.15 RPM
FIN_HG00378	0.51 RPM
GBR_HG00099	0.76 RPM
GBR_HG00111	0.37 RPM
GBR_HG00114	0.63 RPM
GBR_HG00119	0.74 RPM
GBR_HG00131	1.06 RPM
GBR_HG00133	0.43 RPM
GBR_HG00134	0.90 RPM
GBR_HG00137	0.47 RPM
GBR_HG00142	1.11 RPM
GBR_HG00143	0.41 RPM
TSI_NA20512	0.08 RPM
TSI_NA20513	0.75 RPM
TSI_NA20518	0.44 RPM
TSI_NA20532	0.88 RPM
TSI_NA20538	0.64 RPM
TSI_NA20756	0.20 RPM
TSI_NA20765	0.66 RPM
TSI_NA20771	0.31 RPM
TSI_NA20786	0.18 RPM
TSI_NA20798	0.56 RPM
YRI_NA18870	0.47 RPM
YRI_NA18907	0.31 RPM
YRI_NA18916	0.44 RPM
YRI_NA19093	0.42 RPM
YRI_NA19099	0.45 RPM
YRI_NA19114	0.29 RPM
YRI_NA19118	0.44 RPM
YRI_NA19213	0.55 RPM
YRI_NA19214	0.37 RPM
YRI_NA19223	0.72 RPM

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Indel association:

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