RetrogeneDB ID: retro_ptro_2034

Retrocopy location

• Organism: Chimpanzee (Pan troglodytes)
• Coordinates: 4:172161453..172163100(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSPTRG00000040747
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: MTMR9
• Ensembl ID: ENSPTRG00000019986
• Aliases: None
• Description: None

Sequence

>retro_ptro_2034
ATGGAGTTTGCGGAGCTGATTAAGACCCCGCGGGTGGACAATGTGGTGCTGCACCGGCCTTTCTACCCGGCTGTCGAGGG
CACCCTGTGCCTGACGGGCCACCACTTGATCCTGTCCTCCCGGCAGGACAACACGGAGGAGCTGTGGCTCCTCCATTCAA
ACATCGACGCCATCGACAAGCGATTTGTGGGATCACTGGGTACCATCATCATAAAATGTAAAGATTTTCGAATTATTCAG
TTGGATATTCCTGGAATGGAGGAATGCTTGAATATAGCCAGTTCCATTGAGGCATTGTCTACTCTGGACTCCATCACTCT
GATGTACCCTTTCTTTTACCGTCCTATGTTTGAAGTGATAGAAGATGGCTGGCATTCCTTCCTTCCTGAGCAAGAATTTG
AACTCTATTCCTCAGCTACCAGTGAATGGAGGCTAAGCTCTGTCAATAAGGAATTTGCTGTCTGTCCCTCTTACCCACCA
ATTGTCACGGTGCCCAAATCCATCGATGATGAAGCTCTTTGGAAGGTAGCTACATTTCGACATGGAGGGCGCTTCCCAGT
ACTAAGCTATTATCACAAAAAAAATGGGATGGTAATTATGCGAAGTGGTCAGCCACTCACTGGTACAAACGGGAGGAGGT
GCAAGGAAGACGAGAAGCTGATAAATGCTACCCTCAGGGCTGGAAAGCGTGGCTACATCATTGACACCCGATCCCTGAAC
GTGGCTCAGCAAACTAGAGCCAAAGGAGGTGGCTTTGAACAAGAAGCTCATTATCCCCAGTGGAGGCGAATTCGTAAGTC
CATTGAGAGGTATCACATTCTTCAGGAGAGCTTAATCAAACTTGTGGAAGCTTGTAATGACCAAACCCATAACATGGACC
GATGGCTCAGTAAATTGGAGGCCTCTAACTGGCTGACTCACATCAAAGAGATTCTGACAACTGCCTGCCTAGCGGCTCAG
TGCATCGACAGGGAAGGAGCATCAATATTGATTCACGGAACAGAAGGAACTGATTCCACACTTCGGGTGACCTCCCTGGC
CCAGATCATCTTAGAGCCAAGAAGCAGGACCATTCGTGGTTTTGAGGCCCTGATTGAAAGAGAGTGGCTGCAGGCTGGTC
ACCCGTTCCAGCAGCGCTGTGCACAGTCAGCCTACTGTAACACCAAGCAGAAGTGGGAGGCTCCTGTATTTCTTCTCTTC
TTGGACTGCGTGTGGCAGATCCTTCATCAGTTTCCCTGTTCTTTTGAATTTAATGAGAATTTCCTCATCATGCTCTTTGA
GCATGCTTATGCCTCACAGTTTGGAACATTTCTGGGCAACAATGAAAGTGAAAGATGTAAGTTGAAGCTACAGCAGAAGA
CGACGTCTTTGTGGTCCTGGGTTAATCAGCCCAGTGAGCTGAGTAAATTCACCAATCCCCTCTTTGAAGCCAACAACCTT
GTCATCTGGCCTTCAGTTGCTCCGCAGAGTCTTCTGCTGTGGGAAGGTATTTTCCTACGTTGGAATAGATCCTCTAAGTA
TTTGGATGAAGCATATGAAGAAATGGTTAACATCATTGAATATAATAAAGAATTACAAGCAAAAGTCAATATCCTTAGAA
GGCAGTTGGCAGAACTGGAAACAGAGGACAGGATGCAGGAGAGTCCC

Alignment

ORF - retro_ptro_2034 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MEFAELIKTPRVDNVVLHRPFYPAVEGTLCLTGHHLILSSRQDNTEELWLLHSNIDAIDKRFVGSLGTII
          MEFAELIKTPRVDNVVLHRPFYPAVEGTLCLTGHHLILSSRQDNTEELWLLHSNIDAIDKRFVGSLGTII
Retrocopy MEFAELIKTPRVDNVVLHRPFYPAVEGTLCLTGHHLILSSRQDNTEELWLLHSNIDAIDKRFVGSLGTII

Parental  IKCKDFRIIQLDIPGMEECLNIASSIEALSTLDSITLMYPFFYRPMFEVIEDGWHSFLPEQEFELYSSAT
          IKCKDFRIIQLDIPGMEECLNIASSIEALSTLDSITLMYPFFYRPMFEVIEDGWHSFLPEQEFELYSSAT
Retrocopy IKCKDFRIIQLDIPGMEECLNIASSIEALSTLDSITLMYPFFYRPMFEVIEDGWHSFLPEQEFELYSSAT

Parental  SEWRLSYVNKEFAVCPSYPPIVTVPKSIDDEALRKVATFRHGGRFPVLSYYHKKNGMVIMRSGQPLTGTN
          SEWRLS.VNKEFAVCPSYPPIVTVPKSIDDEAL.KVATFRHGGRFPVLSYYH...GMVIMRSGQPLTGTN
Retrocopy SEWRLSSVNKEFAVCPSYPPIVTVPKSIDDEALWKVATFRHGGRFPVLSYYHXXXGMVIMRSGQPLTGTN

Parental  GRRCKEDEKLINATLRAGKRGYIIDTRSLNVAQQTRAKGGGFEQEAHYPQWRRIHKSIERYHILQESLIK
          GRRCKEDEKLINATLRAGKRGYIIDTRSLNVAQQTRAKGGGFEQEAHYPQWRRI.KSIERYHILQESLIK
Retrocopy GRRCKEDEKLINATLRAGKRGYIIDTRSLNVAQQTRAKGGGFEQEAHYPQWRRIRKSIERYHILQESLIK

Parental  LVEACNDQTHNMDRWLSKLEASNWLTHIKEILTTACLAAQCIDREGASILIHGTEGTDSTLQVTSLAQII
          LVEACNDQTHNMDRWLSKLEASNWLTHIKEILTTACLAAQCIDREGASILIHGTEGTDSTL.VTSLAQII
Retrocopy LVEACNDQTHNMDRWLSKLEASNWLTHIKEILTTACLAAQCIDREGASILIHGTEGTDSTLRVTSLAQII

Parental  LEPRSRTIRGFEALIEREWLQAGHPFQQRCAQSAYCNTKQKWEAPVFLLFLDCVWQILRQFPCSFEFNEN
          LEPRSRTIRGFEALIEREWLQAGHPFQQRCAQSAYCNTKQKWEAPVFLLFLDCVWQIL.QFPCSFEFNEN
Retrocopy LEPRSRTIRGFEALIEREWLQAGHPFQQRCAQSAYCNTKQKWEAPVFLLFLDCVWQILHQFPCSFEFNEN

Parental  FLIMLFEHAYASQFGTFLGNNESERCKLKLQQKTMSLWSWVNQPSELSKFTNPLFEANNLVIWPSVAPQS
          FLIMLFEHAYASQFGTFLGNNESERCKLKLQQKT.SLWSWVNQPSELSKFTNPLFEANNLVIWPSVAPQS
Retrocopy FLIMLFEHAYASQFGTFLGNNESERCKLKLQQKTTSLWSWVNQPSELSKFTNPLFEANNLVIWPSVAPQS

Parental  LPLWEGIFLRWNRSSKYLDEAYEEMVNIIEYNKELQAKVNILRRQLAELETEDGMQESP
          L.LWEGIFLRWNRSSKYLDEAYEEMVNIIEYNKELQAKVNILRRQLAELETED.MQESP
Retrocopy LLLWEGIFLRWNRSSKYLDEAYEEMVNIIEYNKELQAKVNILRRQLAELETEDRMQESP

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	0.63 RPM	34.62 RPM
SRP007412_cerebellum	1.25 RPM	22.48 RPM
SRP007412_heart	0.50 RPM	12.39 RPM
SRP007412_kidney	0.39 RPM	8.76 RPM
SRP007412_liver	0.13 RPM	3.47 RPM
SRP007412_testis	14.23 RPM	30.98 RPM

ChIP-Seq

Pan troglodytes was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ptro_2034 retrocopy.

TSS

Pan troglodytes was not studied using FANTOM5 data.

Lab

retro_ptro_2034 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ptro_2034 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Pan troglodytes	ENSPTRG00000019986	1 retrocopy	retro_ptro_2034 ,
Ictidomys tridecemlineatus	ENSSTOG00000020537	1 retrocopy	retro_itri_1574,