RetrogeneDB ID: retro_pabe_1655

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 19:60163437..60164622(+)
• Located in intron of: ENSPPYG00000010489

Retrocopy information

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

Parental gene information

• Parental gene symbol: LETM1
• Ensembl ID: ENSPPYG00000014533
• Aliases: None
• Description: leucine zipper-EF-hand containing transmembrane protein 1 [Source:HGNC Symbol;Acc:6556]

Sequence

>retro_pabe_1655
GATAAGCTGACCCTGGATAACCTGACACAGCTGAAGCTGGTGGCCCTGTGCAAGCTGCTGGAGCTACAGCTTCCTGTGCT
TCCAGCTCACGATGCGGCTGCGCTCCATAAAGGCAGAAGACAAGCTGTTTGCTGAGGAAGGGATGGACAGCCTGAACCTC
AAGGAGCTGCAGGCGGCATGTCGGGCACAAGGCATGCAGGCCCTGGGCGTCAGGGAAAACCTCCTGAGGGGCCAGCTGAA
GCAGTGGCTGGACCTGCACCTGCATCAGGAGATCCCCACATCACTGCTCATCCTGTCCCGGACCATGTACCTCCCGGACA
CCCTCTCACCAGCCGACCAGCTTAAGTCCACACTGCAGACTCTCCCAGAGATTGTGGCAAAGGAAGCACAGGTGAAAGTG
GCCAAGGTGGAGGGCAAGCAGGTGGACAAGGCCAAGCTAGAGGCCACACTGCAGGAGGAGGCGACCATGCAGCAGGAACA
CCGCGAGAAGGAGCTGCAGAAGCGTTCGGAGGTGGCGAAGGATGTTGATCCCGAATGTGTGGAAGCCGCTCCCCAAAGGC
CAGGGGCCCAGCCGCAGCCAGAAGTGCCTGACACAGTCCTGCAGTCAGAGACCCTGAAGGACACTGCCCCCGTGCTGGAG
GGCTTGAAGGAGGAAGAGATTACTAAGGAGGAAATCAACATCTTCAGCGATGCCTGCTCTAAGCTGCAGGAACAGAAGTC
ACTCACCAGGAAGGAGGAGGAGCTGGAGCTGCTGAAGGAGGACATGCAGGACTACAGCGAGGACTTGCAGGAGATCAAGA
AGGAACTTTCAAAGACTGGTGAAGAAAAATACGTGGAAGAATCTAAAGCCAGCAAGAGATTGACAAAAAGGGTGCAGCAG
ATGATCGGGCAGATCGACAGCTTGATCTCAAAGCTGGAGATGGACCAGTGGGCCAGCAAGCTGGCCCCAGCCAAGGGCGT
GCCCATGGGGGAGAACGTCGTCAGTGTCACCGAGCTCATCAACGCCATGAAGCAAGTCAAGCACATTCCCAAAAGCAACC
TCACCAGCCTGGCCGCAGCACTGAATGAAAATAAGGATGGCAAGGTCAACGTCGACCACCTCATCAAGGTGATTGAGCTG
GTGGACAAAGAAGATGTTCATGTCTCCACCAGTCGGTGGCCGAGATTGTAGCAACACTGGAAAAA

Alignment

ORF - retro_pabe_1655 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83. %
• Parental protein coverage: 53.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DNLTRPQLVALCKLLEL-QSIGTNNFLRFQLTMRLRSIKADDKLIAEEGVDSLSVKELQAACRARGMRAL
          D.LT...L..L.KL..L..S.....FL.FQLTMRLRSIKA.DKL.AEEG.DSL..KELQAACRA.GM.AL
Retrocopy DKLTLDNLTQL-KLVAL>ASCWSYSFLCFQLTMRLRSIKAEDKLFAEEGMDSLNLKELQAACRAQGMQAL

Parental  GVTEDRLRGQLKQWLDLHLHQEIPTSLLILSRAMYLPDTLSPADQLKSTLQTLPEIVAKEAQVKAAEVEG
          GV.E..LRGQLKQWLDLHLHQEIPTSLLILSR.MYLPDTLSPADQLKSTLQTLPEIVAKEAQVK.A.VEG
Retrocopy GVRENLLRGQLKQWLDLHLHQEIPTSLLILSRTMYLPDTLSPADQLKSTLQTLPEIVAKEAQVKVAKVEG

Parental  EQVDNKAKLEATLQEEAAIQQEHREKELQKRSEAAKDVEPERVVAAPQRPGTEPQPEMPDTVLQSETLKD
          .QVD.KAKLEATLQEEA..QQEHREKELQKRSE.AKDV.PE.V.AAPQRPG..PQPE.PDTVLQSETLKD
Retrocopy KQVD-KAKLEATLQEEATMQQEHREKELQKRSEVAKDVDPECVEAAPQRPGAQPQPEVPDTVLQSETLKD

Parental  TAPVLEGLKEEEITKEEIDILSDACSKLQEQKKSLTKEKEELELLKEDVQDYSEDLQEIKKELSKTGEEK
          TAPVLEGLKEEEITKEEI.I.SDACSKLQEQK.SLT...EELELLKED.QDYSEDLQEIKKELSKTGEEK
Retrocopy TAPVLEGLKEEEITKEEINIFSDACSKLQEQK-SLTRKEEELELLKEDMQDYSEDLQEIKKELSKTGEEK

Parental  YVEESKASKRLTKRVQQMIGQIDGLISQLEMDQQAGKLAPANGMPTGENIISVAELINAMKQVKHIPESK
          YVEESKASKRLTKRVQQMIGQID.LIS.LEMDQ.A.KLAPA.G.P.GEN..SV.ELINAMKQVKHIP.S.
Retrocopy YVEESKASKRLTKRVQQMIGQIDSLISKLEMDQWASKLAPAKGVPMGENVVSVTELINAMKQVKHIPKSN

Parental  LTSLAAALDENKDGKVNINDLVKVIELVDKEDVHISTSQ-VAEIVATLEK
          LTSLAAAL.ENKDGKVN...L.KVIELVDKEDVH.STS..VAEIVATLEK
Retrocopy LTSLAAALNENKDGKVNVDHLIKVIELVDKEDVHVSTSR<VAEIVATLEK

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	1.66 RPM	34.17 RPM
SRP007412_cerebellum	1.58 RPM	25.05 RPM
SRP007412_heart	0.15 RPM	8.46 RPM
SRP007412_kidney	0.33 RPM	18.46 RPM
SRP007412_liver	0.12 RPM	9.98 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_1655 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_1655 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_1655 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_2019

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Parental genes homology:

Parental genes homology involve 7 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000001859	1 retrocopy	retro_cjac_1529,
Homo sapiens	ENSG00000168924	1 retrocopy	retro_hsap_2019,
Gorilla gorilla	ENSGGOG00000002923	2 retrocopies	retro_ggor_1158, retro_ggor_1159,
Nomascus leucogenys	ENSNLEG00000000067	2 retrocopies	retro_nleu_1752, retro_nleu_2731,
Otolemur garnettii	ENSOGAG00000014883	1 retrocopy	retro_ogar_20,
Pongo abelii	ENSPPYG00000014533	1 retrocopy	retro_pabe_1655 ,
Ictidomys tridecemlineatus	ENSSTOG00000014167	1 retrocopy	retro_itri_160,