RetrogeneDB ID: retro_olat_29

Retrocopy location

• Organism: Medaka (Oryzias latipes)
• Coordinates: 17:8891749..8893441(-)
• Located in intron of: ENSORLG00000006266

Retrocopy information

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

Parental gene information

• Parental gene symbol: GNL3L
• Ensembl ID: ENSORLG00000014117
• Aliases: None
• Description: None

Sequence

>retro_olat_29
ATGTCTAAAGCAAAACAAAAACGTGCCAAACGTCTAGGTTTCCTCGGAAATAAGACGAAAGATGCACAGAAGGGCCATGG
TCTAGGGGGGACAAGGACCTCAGCTGTTCAGCAAACAAAAGACTCCAGAAAGCCAGAGGAAGTCAGGAAACAAAGACTTC
AGAATCTGCAGGAAAAGCAGAAGCTGTCAAGAGAACGTGAGATGATGAAGAGAAGAAACTTACAGAGCTTTCAGGAGGAC
ATCCTGCTGAGGCAAAGAGAGTTTGAACAGAAGGAGACGGAGATGAGGAGTTTGGAGAAGCATGTAAATTTTGAAAATGA
AAATTCAAGAAAAGCATATTACAGAGAGTTTAAAAAGGTTGTGGAAGCATCTGATGTGATTTTGGAGGTGCTGGATGCTC
GTGACCCTCTGGGCTGCAGATGTCCTCAGGTGGAACAGGCAGTCATCCAGAGTGGAACCAACAAGAAGATAGTATTGGTG
CTTAATAAAATAGATTTGGTGTCAAAGGAAATTGTGGAGAAATGGATTAAGTATCTTCGGAATGAGTTTCCTACTGTGGC
TTTTAAAGCATCCACGCAGCAACAAGCAAAGAACCTGAAACGCAGTAATGTGTCGGTGACCCAGGCCACCGCAGAGCTTC
TCAGCACCAGTGCCTGTATTGGAGCGGACTGCCTGATGAGGTTACTTGGTAATTATTGTCGCAACCAGGACATCAAGACA
GCCATCACTGTTGGTGTTGTGGGTTTTCCAAATGTGGGAAAGAGCAGTTTAATCAACAGCCTGAAACGAGCACGAGCATG
TCACGTCGGCGCCACCCCGGGTGTAACAAAGTGCCTTCAAGAGGTACATTTGGACAAACACATTAAACTTCTCGACTGCC
CCGGTATCGTCATGGCAACCTCAACAAGTGACGCGGTGATGATTCTCCGCAACTGTGTGAAGATTGAACAGCTGGTAGAT
CCTCTGCCGCCTGTTGAGGCCATCCTACGGCGATGCAACAAAGTCCAGATCATGGAGCATTACGGCGTTCCCGACTTTCA
GACAGCTGCAGAGTTCTTGGCAATGCTCGCCAGGCGTCAAGGCAAATTAAGAAAAGGAGGTCTGCCAGACACAGACAAAG
CAGCCAAGAGTGTGTTGATGGACTGGACAGGGGGACGCATCACTTATTTCACACACCCTCCAGAGACGCACACTCTCCCC
ACTCATGTCAGTGCTGAGATTGTAACAGAGATGGGAAAAGCTTTCAACTGGGATGAGCTGGAAAAGGGAAATCAGGAGGT
TCTTGCAGAGTCGTCTTGCCCTGATGTCCAAATGGGCTTTTGTATGGAGTCCATTGGAATGACACAAGGTGATCACGAGG
AGCCACACTTTGGTCTACAGATTGAAGGAGGCTCCGGGGCAGAGCCAACAGCAGAAGATAAAACTGAGTTTATGGAAGAT
GATCAAGATCCAGAATTTGGACCAATGACAGTGGAGTTCAAATCACAGAAGGTGAACCGTTTACCCGTGAGTGAAGCAGC
TCCCCGGACTCCGAGTTTAGAGGACATTTTTGATATAGATCCTTTACAACAAGGCCATGCAATGCTGGCTGCCAACAAGA
AGAGGAAAAAAAAGCAAAAAAGAGCCGACAAAATTGCCACAAAGCTCTCCGATACTCTGACATCTGCCATGGATTTCTCA
TTTTCAGATCCC

Alignment

ORF - retro_olat_29 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.94 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSKAKQKRAKRLGFLGNKTKDAQKGHGLGGTRTSAVQQTKDSRKPEEVRKQRLQNLQEKQKLSREREMMK
          MSKAKQKRAKRLGFLGNKTKDAQKGHGLGGTRTSAVQQTKDSRKPEEVRKQRLQNLQEKQKLSREREMMK
Retrocopy MSKAKQKRAKRLGFLGNKTKDAQKGHGLGGTRTSAVQQTKDSRKPEEVRKQRLQNLQEKQKLSREREMMK

Parental  RRNLQSFQEDILLRQREFEQKETEMRSLEKHVNFENENSRKAYYREFKKVVEASDVILEVLDARDPLGCR
          RRNLQSFQEDILLRQREFEQKETEMRSLEKHVNFENENSRKAYYREFKKVVEASDVILEVLDARDPLGCR
Retrocopy RRNLQSFQEDILLRQREFEQKETEMRSLEKHVNFENENSRKAYYREFKKVVEASDVILEVLDARDPLGCR

Parental  CPQVEQAVIQSGTNKKIVLVLNKIDLVSKEIVEKWIKYLRNEFPTVAFKASTQQQAKNLKRSNVSVTQAT
          CPQVEQAVIQSGTNKKIVLVLNKIDLVSKEIVEKWIKYLRNEFPTVAFKASTQQQAKNLKRSNVSVTQAT
Retrocopy CPQVEQAVIQSGTNKKIVLVLNKIDLVSKEIVEKWIKYLRNEFPTVAFKASTQQQAKNLKRSNVSVTQAT

Parental  AELLSTSACIGADCLMRLLGNYCRNQDIKTAITVGVVGFPNVGKSSLINSLKRARACHVGATPGVTKCLQ
          AELLSTSACIGADCLMRLLGNYCRNQDIKTAITVGVVGFPNVGKSSLINSLKRARACHVGATPGVTKCLQ
Retrocopy AELLSTSACIGADCLMRLLGNYCRNQDIKTAITVGVVGFPNVGKSSLINSLKRARACHVGATPGVTKCLQ

Parental  EVHLDKHIKLLDCPGIVMATSTSDAVMILRNCVKIEQLVDPLPPVEAILRRCNKVQIMEHYGVPDFQTAA
          EVHLDKHIKLLDCPGIVMATSTSDAVMILRNCVKIEQLVDPLPPVEAILRRCNKVQIMEHYGVPDFQTAA
Retrocopy EVHLDKHIKLLDCPGIVMATSTSDAVMILRNCVKIEQLVDPLPPVEAILRRCNKVQIMEHYGVPDFQTAA

Parental  EFLAMLARRQGKLRKGGLPDTDKAAKSVLMDWTGGRITYFTHPPETHTLPTHVSAEIVTEMGKAFNWDEL
          EFLAMLARRQGKLRKGGLPDTDKAAKSVLMDWTGGRITYFTHPPETHTLPTHVSAEIVTEMGKAFNWDEL
Retrocopy EFLAMLARRQGKLRKGGLPDTDKAAKSVLMDWTGGRITYFTHPPETHTLPTHVSAEIVTEMGKAFNWDEL

Parental  EKGNQEVLAESSCPDVQMGFCMESIGMTQGDHEEPHFGLQIEGGSGAEPTAEDKTEFMEDDQDPEFGPMT
          EKGNQEVLAESSCPDVQMGFCMESIGMTQGDHEEPHFGLQIEGGSGAEPTAEDKTEFMEDDQDPEFGPMT
Retrocopy EKGNQEVLAESSCPDVQMGFCMESIGMTQGDHEEPHFGLQIEGGSGAEPTAEDKTEFMEDDQDPEFGPMT

Parental  VEFKSQKVNRLPVSEAAPRTPSLEDIFDIDPLQQGHAMLAANKKRKKKQKRADKIATKLSDTLTSAMDFS
          VEFKSQKVNRLPVSEAAPRTPSLEDIFDIDPLQQGHAMLAANKKR......ADKIATKLSDTLTSAMDFS
Retrocopy VEFKSQKVNRLPVSEAAPRTPSLEDIFDIDPLQQGHAMLAANKKRXXXXXXADKIATKLSDTLTSAMDFS

Parental  FSDP
          FSDP
Retrocopy FSDP

Legend:

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

Expression

RNA-Seq

Oryzias latipes was not studied using RNA-Seq expression data.

ChIP-Seq

Oryzias latipes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_olat_29 retrocopy.

TSS

Oryzias latipes was not studied using FANTOM5 data.

Lab

retro_olat_29 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_olat_29 has 0 orthologous retrocopies within teleost group .

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Parental genes homology:

Parental genes homology involve 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000000252	2 retrocopies	retro_cjac_1591, retro_cjac_1853,
Homo sapiens	ENSG00000130119	1 retrocopy	retro_hsap_3327,
Gorilla gorilla	ENSGGOG00000007550	1 retrocopy	retro_ggor_1296,
Microcebus murinus	ENSMICG00000010144	1 retrocopy	retro_mmur_662,
Macaca mulatta	ENSMMUG00000008231	1 retrocopy	retro_mmul_2084,
Nomascus leucogenys	ENSNLEG00000016233	1 retrocopy	retro_nleu_1672,
Oryzias latipes	ENSORLG00000014117	1 retrocopy	retro_olat_29 ,
Pongo abelii	ENSPPYG00000020383	1 retrocopy	retro_pabe_2742,