RetrogeneDB ID: retro_pabe_2651

Retrocopy location

• Organism: Orangutan (Pongo abelii)
• Coordinates: 5:77409137..77410666(+)
• Located in intron of: ENSPPYG00000015576

Retrocopy information

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

Parental gene information

• Parental gene symbol: ALDH7A1
• Ensembl ID: ENSPPYG00000025927
• Aliases: None
• Description: aldehyde dehydrogenase 7 family, member A1 [Source:HGNC Symbol;Acc:877]

Sequence

>retro_pabe_2651
ATGTCCACTCTCCTCATCAATCAGCCCCAGTATGCATGGCTGAAAGAGCTGGGGCTCCGCGAGGAAAACGAGGGCGTGTA
TAATGGAAGCTGGGGAGGCCGGGGAGAGGTTATTATGACCTATTGCCCTGCTAACAACTAGCCAATAGCAAGAGTCCGAC
AGACCAGTGTGGCAGACTATGAAGAAACTGTAAAGAAAGCAAGAGAAGCATGGAAAATCTGGGCAGATATTCCTGCTCCA
AAACGAGGAGAAATAGTAAGACAGATTGGCGATGCCTTGCGGGAGAAGATCCAAGTACTAGGAAGCTTGGTGTCTTTGGA
GATGGGGAAAATCTTAGTGGAAGGTGTGGGTGAAGTTCAGGAGTATGTGGATATCTGTGACTATGCTGTTGGTTTATCAA
GGATGATTGGAGGACCTATCTTGCCTTCTGAAAGACCTGGCCATGCACTGATTGAGCAGTGGAATCCTGTAGGCCTGGTT
GGAATCATCACGGCATTCAGTTTCCCTGTGGCAGTGTATGGTTGGAACAACGCCATTGCCTTGATCTGTGGAAATGTCTG
CTTCTGGAAAGGAGCTCCAACCACTTCCCTCATTAGTGTGGCTGTCACAAAGATAATAGCCAAGGTTCTGGAGGACAAGC
TGCCTGGTGCAATTTATTCCTTGACTTGTGGTGGAGCAGATATTGGCACAGCAATGGCCAAAGATGAACGAGTGAACCTG
CTGTCCTTCACTGGGAGCACTCAGGTGGGAAAACAGGTGACCCTGATGGTGCAGGAGAGGTTTGGGAGAAGTTTGTTGGA
ACTTGGAGGAAACAATGCCATTATTGCCTTTGAAGATGCAGACCTCAGCTTAGTTGTTCCATCAGCTCTCTTCACTGCTG
TGGGAACAGCTGGCCAGAGGTGTACCACTGCAAGGCGACTGTTTGTACATGAAAGCATCCATGATGAGGTTGTAAACAGA
CTTAAAAAGGCCTATGCACAGATCCGAGTTGGGAACCCATGGGACCCTAATGTTCTCTATGGGCCACTCCACACCAAACA
GGCAGTGAGCATGTTTCTTGGAGCAGTGGAAGAAGCAAAAAAAGAAGGTGGCACAGTGGTCTATGGGGGCAAGGTTATGG
ATCGCCCTGGAAATTACGTAGAACCGACAATTGTGACAGGTCTTGCCCACGATGCATCCACTGCACACACAGAGACTTTT
GCTCCGATTCTCTATGTCTTTAAGTTCAAGAATGAAGAAGAGGTCTTTGCATGGAATAGTGAAGTAAAACAGGGACTTTC
AAGTAGCATCTTTACCAAAGATCTGAGCAGAATCTTTCGCTGGCTTGGACCTAAAGATCAGACTGTGGCATTGTAAATGT
CAACATTCCAACAAGTGGGGCTGAGATTGGAGGTGCATTTGGAGGAGAAAAGCACACTGGTGGTGGCAGGGAGTCTGGCA
GTGATGCCTGGAAACAGTACATGAGAAGGTCTACTTGTACTATCAACTACAGTAAAGACTTTCCTCTGGCCCAAGGAATC
AAGTTTCAG

Alignment

ORF - retro_pabe_2651 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.9 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSTLLINQPQYAWLKELGLREENEGVYNGSWGGQGEVITTYCPANNEPIARVRQASVADYEETIKKAREA
          MSTLLINQPQYAWLKELGLREENEGVYNGSWGG.GEVI.TYCPANN.PIARVRQ.SVADYEET.KKAREA
Retrocopy MSTLLINQPQYAWLKELGLREENEGVYNGSWGGRGEVIMTYCPANN*PIARVRQTSVADYEETVKKAREA

Parental  WKIWADIPAPKRGEIVRQIGDALREKIQVLRSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPI
          WKIWADIPAPKRGEIVRQIGDALREKIQVL.SLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPI
Retrocopy WKIWADIPAPKRGEIVRQIGDALREKIQVLGSLVSLEMGKILVEGVGEVQEYVDICDYAVGLSRMIGGPI

Parental  LPSERPGHALIEQWNPVGLVGIITAFNFPVAVYGWNNAIAMICGNVCLWKGAPTTSLISVAVTKIIAKVL
          LPSERPGHALIEQWNPVGLVGIITAF.FPVAVYGWNNAIA.ICGNVC.WKGAPTTSLISVAVTKIIAKVL
Retrocopy LPSERPGHALIEQWNPVGLVGIITAFSFPVAVYGWNNAIALICGNVCFWKGAPTTSLISVAVTKIIAKVL

Parental  EDNKLPGAICSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVALMVQERFGRSLLELGGNNAIIAFED
          ED.KLPGAI.SLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQV.LMVQERFGRSLLELGGNNAIIAFED
Retrocopy ED-KLPGAIYSLTCGGADIGTAMAKDERVNLLSFTGSTQVGKQVTLMVQERFGRSLLELGGNNAIIAFED

Parental  ADLSLVVPSALFAAVGTAGQRCTTVRRLFVHESIHDEVVNRLKKAYAQIRVGNPWDSNVLYGPLHTKQAV
          ADLSLVVPSALF.AVGTAGQRCTT.RRLFVHESIHDEVVNRLKKAYAQIRVGNPWD.NVLYGPLHTKQAV
Retrocopy ADLSLVVPSALFTAVGTAGQRCTTARRLFVHESIHDEVVNRLKKAYAQIRVGNPWDPNVLYGPLHTKQAV

Parental  SMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLAHDASIAHTETFAPILYVFKFKNEEEVFAWN
          SMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLAHDAS.AHTETFAPILYVFKFKNEEEVFAWN
Retrocopy SMFLGAVEEAKKEGGTVVYGGKVMDRPGNYVEPTIVTGLAHDASTAHTETFAPILYVFKFKNEEEVFAWN

Parental  NEVKQGLSSSIFTKDLGRIFRWLGPKG-SDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM
          .EVKQGLSSSIFTKDL.RIFRWLGPK..SDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM
Retrocopy SEVKQGLSSSIFTKDLSRIFRWLGPKD<SDCGIVNVNIPTSGAEIGGAFGGEKHTGGGRESGSDAWKQYM

Parental  RRSTCTINYSKDLPLAQGIKFQ
          RRSTCTINYSKD.PLAQGIKFQ
Retrocopy RRSTCTINYSKDFPLAQGIKFQ

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	2.10 RPM	32.18 RPM
SRP007412_cerebellum	1.22 RPM	16.42 RPM
SRP007412_heart	1.81 RPM	13.28 RPM
SRP007412_kidney	6.93 RPM	67.59 RPM
SRP007412_liver	4.10 RPM	47.00 RPM

ChIP-Seq

Pongo abelii was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_pabe_2651 retrocopy.

TSS

Pongo abelii was not studied using FANTOM5 data.

Lab

retro_pabe_2651 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_pabe_2651 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3196

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Parental genes homology:

Parental genes homology involve 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002143	1 retrocopy	retro_chof_869,
Homo sapiens	ENSG00000164904	1 retrocopy	retro_hsap_3196,
Pongo abelii	ENSPPYG00000004966	1 retrocopy	retro_pabe_32,
Pongo abelii	ENSPPYG00000025927	1 retrocopy	retro_pabe_2651 ,
Sarcophilus harrisii	ENSSHAG00000013162	1 retrocopy	retro_shar_758,