RetrogeneDB ID: retro_pabe_144

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 13_random:5834418..5836536(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPPYG00000025934
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSPPYG00000005719
• Aliases: None
• Description: None

Sequence

>retro_pabe_144
ATGAATGAAAGTAAACCTGGTGACTCACAGAACCTTGCTTGTGTTTTCTGTCGAAAAAATGATGACTGTCCTAATAAATA
TGGAGAAAAGAAAACTAAGGAGAAATGGAATCTCACTGTACATTACTACTGTTTGTTGATGTCAAGTGGAATTTGGCAGA
GAGGCAAAGAAGAAGAAGGAGTTTATGGTTTTCTAATAGAAGATATCAGGAAGGAAGTGAATAGAGCTTCTAAACTGAAA
TGCTGTGTTTGCAAGAAAAATGGTGCTTCAATTGGATGTGTTGCACCCCGATGTAAACGAAGTTATCATTTCCCATGTGG
ACTTCAGAGAGAATGTATTTTCCAGTTTACTGGCAATTTTGCGTCATTTTGTTGGGACCATCGACCTGTTCAAATAATTA
CATCTAATAATTATAGAGAGTCCTTACCATGCACCATTTGCTTGGAATTTATTGAGCCTATTCCAAGTTATAACATATTA
CGAAGTCCTTGTTGTAAGAACGCTTGGTTTCATAGAGACTGTTTACAGGTTCAAGCAATAAATGCGGGAGTGTTTTTCTT
TAGGTGTACAATATGCAATAATAGTGACATCTTTCAGAAAGAGATGTTGAGAATGGGAATTCATATTCCTGAAAAAGATG
CTTCCTGGGAATTAGAGGAAAACGCTTATCAAGAGCTTCTGCAGCACTATGAGCGTTGTGATGTTCGAAGATGTCGTTGC
AAAGAAGGGCGAGACTATAATGCATCTGATAGCAAATGGGAAATAAAGCGCTGTCAGTGTTGTGGTTCCAGTGGCACACA
TTTAGCCTGCTCCTCATTACGGTCATGGGAGCAAAATTGGGAGTGTTTGGAATGTAGGGGTATTATCTACAATTCAGGAG
ATTTCCAAAAAGCCAAAAAACGTGTATTACCCAACTCTAATAATGTGGGGATTACAGATTGTTTATTGGAAGAGTCATCA
CCTAAATTACCCAGACAGTCACCTGGAGCCCAGAGTAAAGATCTACTGAGGCAAGGCAGCAAATTTAGAAGAAATGTATC
AACACTATTAATAGAGTTAGGATTCCAAATTAAAAAAAAAACTAAAAGATTATATATCAACAAAGCCAATATCTGGAATA
GTGCCTTAGATGCATTCAGAAATCGAAACTTTAATCCTTCATATGCAATTGAAGTAGCATATGTTATTGAAAATGATAAT
TTTGGAAGTGAGCATCCTGGATCAAAGCAAGAATTTCTGAGTCTCTTAATGCAACATCTTGAGAACTCATCATTGTTTGA
AGGGTCCTTGTCAAAGAACTTGTCTCTAAATTCTCAAGCTCTGAAAGAGAATCTTTACTATGAAGCTGGCAAAATGCTTG
CCATTTCTTTAGTTCACGGTGGTCCTTCACCTGGTTTCTTTTCTAAAACCTTGTTTAACTGCCTTGTTTATGGACCAGAA
AATACCCAGCCAATTTTAGATGATGTTTCAGACTTTGATGTGGCACAGATTATAATCAGGATAAACACTGCAACAACTGT
AGCTGACTTAAAGTCAATAATAAATGAATGCTATAACTACCTTGAGTTAATTGGATGTCTCAGACTTATAACGACATTAA
GTGATAAATATATGTTAGTAAAAGACATACTTGTCTACCATGTAATTCAGAGAGTCCACGCACCCTTTGAAAGTTTCAAG
CAGGGTCTGAAAACCCTTGGTGTTTTGGAGAAAATTCAGGCTTATCCAGAAGCATTTTGTAGCATCCTGTGTCATAAACC
TGAGAGTCTTTCTGCAAAAATCCTTAGTGAGCTTTTTACAGTACACACATTACCTGATGTAAAAGCTTTGGGGTTTTGGA
ACAGTTACTTACAGGCTGTTGAAGATGGTAAATCTACAACAACAATGGAAGACATTCTTATTTTTGCAACTGGTTGCAGT
TCCATTCCTCCAGCTGGATTTAAACCCACTCCTTCAATTGAGTGTCTGCATGTGGATTTTCCTGTTGGAAACAAGTGTAA
TAACTGTTTAGCAATTCCCATCACCAATACATATAAAGAGTTTCAAGAGAATATGGACTTCACCATAAGAAACACTCTAA
GACTAGGAAAGGAAGAAAGTTCTCATTACATTGGACAT

Alignment

ORF - retro_pabe_144 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNESKPGDSQNLACVFCRKNDDCPNKYGEKKTKEKWNLTVHYYCLLMSSGIWQRGKEEEGVYGFLIEDIR
          MNESKPGDSQNLACVFCRKNDDCPNKYGEKKTKEKWNLTVHYYCLLMSSGIWQRGKEEEGVYGFLIEDIR
Retrocopy MNESKPGDSQNLACVFCRKNDDCPNKYGEKKTKEKWNLTVHYYCLLMSSGIWQRGKEEEGVYGFLIEDIR

Parental  KEVNRASKLKCCVCKKNGASIGCVAPRCKRSYHFPCGLQRECIFQFTGNFASFCWDHRPVQIITSNNYRE
          KEVNRASKLKCCVCKKNGASIGCVAPRCKRSYHFPCGLQRECIFQFTGNFASFCWDHRPVQIITSNNYRE
Retrocopy KEVNRASKLKCCVCKKNGASIGCVAPRCKRSYHFPCGLQRECIFQFTGNFASFCWDHRPVQIITSNNYRE

Parental  SLPCTICLEFIEPIPSYNILRSPCCKNAWFHRDCLQVQAINAGVFFFRCTICNNSDIFQKEMLRMGIHIP
          SLPCTICLEFIEPIPSYNILRSPCCKNAWFHRDCLQVQAINAGVFFFRCTICNNSDIFQKEMLRMGIHIP
Retrocopy SLPCTICLEFIEPIPSYNILRSPCCKNAWFHRDCLQVQAINAGVFFFRCTICNNSDIFQKEMLRMGIHIP

Parental  EKDASWELEENAYQELLQHYERCDVRRCRCKEGRDYNAPDSKWEIKRCQCCGSSGTHLACSSLRSWEQNW
          EKDASWELEENAYQELLQHYERCDVRRCRCKEGRDYNA.DSKWEIKRCQCCGSSGTHLACSSLRSWEQNW
Retrocopy EKDASWELEENAYQELLQHYERCDVRRCRCKEGRDYNASDSKWEIKRCQCCGSSGTHLACSSLRSWEQNW

Parental  ECLECRGIIYNSGDFQKAKKHVLPNSNNVGITDCLLEESSPKLPRQSPGAQSKDLLRQGSKFRRNVSTLL
          ECLECRGIIYNSGDFQKAKK.VLPNSNNVGITDCLLEESSPKLPRQSPGAQSKDLLRQGSKFRRNVSTLL
Retrocopy ECLECRGIIYNSGDFQKAKKRVLPNSNNVGITDCLLEESSPKLPRQSPGAQSKDLLRQGSKFRRNVSTLL

Parental  IELGFQIKKKTKRLYINKANIWNSALDAFRNRNFNPSYAIEVAYVIENDNFGSEHPGSKQEFLSLLMQHL
          IELGFQIKKKTKRLYINKANIWNSALDAFRNRNFNPSYAIEVAYVIENDNFGSEHPGSKQEFLSLLMQHL
Retrocopy IELGFQIKKKTKRLYINKANIWNSALDAFRNRNFNPSYAIEVAYVIENDNFGSEHPGSKQEFLSLLMQHL

Parental  ENSSLFEGSLSKNLSLNSQALKENLYYEAGKMLAISLVHGGPSPGFFSKTLFNCLVYGPENTQPILDDVS
          ENSSLFEGSLSKNLSLNSQALKENLYYEAGKMLAISLVHGGPSPGFFSKTLFNCLVYGPENTQPILDDVS
Retrocopy ENSSLFEGSLSKNLSLNSQALKENLYYEAGKMLAISLVHGGPSPGFFSKTLFNCLVYGPENTQPILDDVS

Parental  DFDVAQIIIRINTATTVADLKSIINECYNYLELIGCLRLITTLSDKYMLVKDILVYHVIQRVHAPFESFK
          DFDVAQIIIRINTATTVADLKSIINECYNYLELIGCLRLITTLSDKYMLVKDILVYHVIQRVHAPFESFK
Retrocopy DFDVAQIIIRINTATTVADLKSIINECYNYLELIGCLRLITTLSDKYMLVKDILVYHVIQRVHAPFESFK

Parental  QGLKTLGVLEKIQAYPEAFCSILCHKPESLSAKILSELFTVHTLPDVKALGFWNSYLQAVEDGKSTTTME
          QGLKTLGVLEKIQAYPEAFCSILCHKPESLSAKILSELFTVHTLPDVKALGFWNSYLQAVEDGKSTTTME
Retrocopy QGLKTLGVLEKIQAYPEAFCSILCHKPESLSAKILSELFTVHTLPDVKALGFWNSYLQAVEDGKSTTTME

Parental  DILIFATGCSSIPPAGFKPTPSIECLHVDFPVGNKCNNCLAIPITNTYKEFQENMDFTIRNTLRLGKEES
          DILIFATGCSSIPPAGFKPTPSIECLHVDFPVGNKCNNCLAIPITNTYKEFQENMDFTIRNTLRLGKEES
Retrocopy DILIFATGCSSIPPAGFKPTPSIECLHVDFPVGNKCNNCLAIPITNTYKEFQENMDFTIRNTLRLGKEES

Parental  SHYIGH
          SHYIGH
Retrocopy SHYIGH

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	0.28 RPM	0.94 RPM
SRP007412_cerebellum	0.36 RPM	2.07 RPM
SRP007412_heart	0.15 RPM	0.48 RPM
SRP007412_kidney	0.07 RPM	0.33 RPM
SRP007412_liver	0.09 RPM	0.40 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_144 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_144 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_144 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002109	1 retrocopy	retro_chof_341,
Homo sapiens	ENSG00000092140	1 retrocopy	retro_hsap_2706,
Pongo abelii	ENSPPYG00000005719	1 retrocopy	retro_pabe_144 ,
Pan troglodytes	ENSPTRG00000006234	1 retrocopy	retro_ptro_1827,